They also show that nine asset managers shared a total of £986,000 in 2017.

Joy's bonus came despite the charity failing to hit its target of a 9.1 per cent total return on investments. It achieved 7.1 per cent.

Investable assets, however, grew from £7.9bn to £8.3bn.

The charity’s overall income grew from £159.6m in 2016 to £167.3m last year, the accounts show.

Joy's salary would rank him fifth in a list of the charity sector's biggest earners.

According to Third Sector's Charity Pay Study 2017, which was based on analysis of the accounts of the 150 largest charities by income in England and Wales, the Wellcome Trust topped the league with its highest-paid earner taking home just over £3m.

The Church Commissioners for England's large bonuses were paid despite Justin Welby, the Archbishop of Canterbury, urging companies to show pay restraint.

The charity also used its latest annual report to highlight how it uses its votes at company AGMs and meetings to prevent excessive pay elsewhere.

The report says: "The Commissioners and Pensions Board vote in over 2,500 company meetings each year.

"In 2017, we voted against 50 per cent of remuneration packages in the UK."

But a Church Commissioners for England spokeswoman said its remuneration policy was "entirely consistent" with its approach to other companies.

She said: "The payment is largely made up of long-term incentive payments that are assessed over a five-year period.

"These payments are paid out on the sixth year at 75 per cent and the remaining 25 per cent over the next two years.

"The increase is therefore to do with past performance, not this year’s.

Peter Vicary-Smith, chief executive of Which?, whose £462,000 pay packet drew criticism, announced this month that he would step down in September.

In February, the disability car charity Motability was criticised after a connected company, Motability Operations Group, was found to have paid its chief executive £1.7m in the year to 30 September 2017, including a long-term incentive scheme payment of almost £727,000.